I've tried to work with these in both health science and agricultural industries. The bottlenecks are the reasoning they support and the quality of the data be

I've tried to work with these in both health science and agricultural industries. The bottlenecks are the reasoning they support and the quality of the data being annotated with the ontologies. The long and the short of it is that every organization is going to partially disagree with the subtleties of certain categorizations which proliferates standards and ad-hoc modifications. There needs to be means of adjusting mappings at runtime and to store changes. It also needs to be so stupid/simple that an old-guard biologist can use it and immediately comprehend the value. Querying ontologies is easy, working with annotations-qua-annotations is more difficult than it has to be, and as such organizations typically will want to roll their own.